diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf index 4a7f0097..67384b0c 100644 --- a/modules/chromap/chromap/main.nf +++ b/modules/chromap/chromap/main.nf @@ -1,13 +1,11 @@ -def VERSION = '0.1' // Version information not provided by tool on CLI - process CHROMAP_CHROMAP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null) + conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' : - 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' : + 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }" input: tuple val(meta), path(reads) @@ -45,7 +43,7 @@ process CHROMAP_CHROMAP { args_list << "--pairs-natural-chr-order $pairs_chr_order" } def final_args = args_list.join(' ') - def compression_cmds = "gzip ${prefix}.${file_extension}" + def compression_cmds = "gzip -n ${prefix}.${file_extension}" if (args.contains("--SAM")) { compression_cmds = """ samtools view $args2 -@ $task.cpus -bh \\ @@ -67,7 +65,8 @@ process CHROMAP_CHROMAP { cat <<-END_VERSIONS > versions.yml "${task.process}": - chromap: $VERSION + chromap: \$(echo \$(chromap --version 2>&1)) + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } else { @@ -85,7 +84,8 @@ process CHROMAP_CHROMAP { cat <<-END_VERSIONS > versions.yml "${task.process}": - chromap: $VERSION + chromap: \$(echo \$(chromap --version 2>&1)) + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } diff --git a/modules/vcfanno/main.nf b/modules/vcfanno/main.nf new file mode 100644 index 00000000..421fc0fa --- /dev/null +++ b/modules/vcfanno/main.nf @@ -0,0 +1,34 @@ +process VCFANNO { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': + 'quay.io/biocontainers/vcfanno:0.3.3--h9ee0642_0' }" + + input: + tuple val(meta), path(vcf), path(tbi) + path vcfanno_config + + output: + tuple val(meta), path("*.vcf"), emit: vcf + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + vcfanno \\ + -p $task.cpus \\ + $args \\ + $vcfanno_config \\ + $vcf \\ + > ${prefix}_annotated.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) + END_VERSIONS + """ +} diff --git a/modules/vcfanno/meta.yml b/modules/vcfanno/meta.yml new file mode 100644 index 00000000..bbd2ab16 --- /dev/null +++ b/modules/vcfanno/meta.yml @@ -0,0 +1,56 @@ +name: vcfanno +description: quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files +keywords: + - vcf + - bed + - annotate + - variant +tools: + - vcfanno: + description: annotate a VCF with other VCFs/BEDs/tabixed files + homepage: None + documentation: https://github.com/brentp/vcfanno#vcfanno + tool_dev_url: https://github.com/brentp/vcfanno + doi: "10.1186/s13059-016-0973-5" + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: query VCF file + pattern: "*.{vcf.gz}" + - vcf.tbi: + type: file + description: query VCF file index + pattern: "*.{vcf.gz.tbi}" + - vcfanno_config: + type: file + description: | + A simple configuration file is used to specify both the source files + and the set of attributes (in the case of VCF) + or columns (in the case of BED or other tab-delimited formats) + that should be added to the query file. + pattern: "*.{toml}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: Annotated VCF file + pattern: "*.{vcf}" + +authors: + - "@projectoriented" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index fc062e58..967b7d9f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1493,6 +1493,10 @@ variantbam: - modules/variantbam/** - tests/modules/variantbam/** +vcfanno: + - modules/vcfanno/** + - tests/modules/vcfanno/** + vcflib/vcfuniq: - modules/vcflib/vcfuniq/** - tests/modules/vcflib/vcfuniq/** diff --git a/tests/modules/chromap/chromap/test.yml b/tests/modules/chromap/chromap/test.yml index 20a51e2b..09e5e753 100644 --- a/tests/modules/chromap/chromap/test.yml +++ b/tests/modules/chromap/chromap/test.yml @@ -5,9 +5,8 @@ - chromap files: - path: output/chromap/genome.index - md5sum: f889d5f61d80823766af33277d27d386 - path: output/chromap/test.bed.gz - md5sum: 7029066c27ac6f5ef18d660d5741979a + md5sum: 25e40bde24c7b447292cd68573728694 - name: chromap chromap test_chromap_chromap_paired_end command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config @@ -16,9 +15,8 @@ - chromap files: - path: output/chromap/genome.index - md5sum: f889d5f61d80823766af33277d27d386 - path: output/chromap/test.bed.gz - md5sum: cafd8fb21977f5ae69e9008b220ab169 + md5sum: 7cdc8448882b75811e0c784f5f20aef2 - name: chromap chromap test_chromap_chromap_paired_bam command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config @@ -27,6 +25,5 @@ - chromap files: - path: output/chromap/genome.index - md5sum: f889d5f61d80823766af33277d27d386 - path: output/chromap/test.bam - md5sum: bd1e3fe0f3abd1430ae191754f16a3ed + md5sum: 73e2c76007e3c61df625668e01b3f42f diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml index dde1aa1b..430a53b7 100644 --- a/tests/modules/chromap/index/test.yml +++ b/tests/modules/chromap/index/test.yml @@ -5,3 +5,5 @@ - chromap files: - path: output/chromap/genome.index + + diff --git a/tests/modules/vcfanno/main.nf b/tests/modules/vcfanno/main.nf new file mode 100644 index 00000000..c46afa8f --- /dev/null +++ b/tests/modules/vcfanno/main.nf @@ -0,0 +1,19 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { VCFANNO } from '../../../modules/vcfanno/main.nf' + +workflow test_vcfanno { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + ] + + toml = file("https://raw.githubusercontent.com/nf-core/test-datasets/8fbd9f99a2feb3f9e39cd3bcdc4a9176a5835673/data/delete_me/vcfanno.toml", + checkIfExists: true) + + VCFANNO ( input, toml ) +} diff --git a/tests/modules/vcfanno/nextflow.config b/tests/modules/vcfanno/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/vcfanno/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/vcfanno/test.yml b/tests/modules/vcfanno/test.yml new file mode 100644 index 00000000..0b5394d2 --- /dev/null +++ b/tests/modules/vcfanno/test.yml @@ -0,0 +1,9 @@ +- name: vcfanno test_vcfanno + command: nextflow run tests/modules/vcfanno -entry test_vcfanno -c tests/config/nextflow.config + tags: + - vcfanno + files: + - path: output/vcfanno/test_annotated.vcf + md5sum: 34259cf6b0a4698a2917ad3554b50c0f + - path: output/vcfanno/versions.yml + md5sum: 62d13540503b22f04a2280c91942cb03